Add --sam-omit-prim-seq

MANUAL

@@ -1423,6 +1423,12 @@ must also be specified. This is because the ID tag is required by the
 SAM Spec. Specify --rg multiple times to set multiple fields. See the
 SAM Spec for details about what fields are legal.
 
+    --sam-omit-prim-seq
+
+When printing primary alignments, Bowtie 2 by default will write out
+the SEQ and QUAL strings. Specifying this option causes Bowtie 2 to
+print an asterisk in those fields instead.
+
     --omit-sec-seq
 
 When printing secondary alignments, Bowtie 2 by default will write out

MANUAL.markdown

@@ -1822,6 +1822,17 @@ must also be specified.  This is because the `ID` tag is required by the [SAM
 Spec][SAM].  Specify `--rg` multiple times to set multiple fields.  See the
 [SAM Spec][SAM] for details about what fields are legal.
 
+</td></tr>
+<tr><td id="bowtie2-options-sam-omit-prim-seq">
+
+    --sam-omit-prim-seq
+
+</td><td>
+
+When printing primary alignments, Bowtie 2 by default will write out
+the `SEQ` and `QUAL` strings. Specifying this option causes Bowtie 2 to
+print an asterisk in those fields instead.
+
 </td></tr>
 <tr><td id="bowtie2-options-omit-sec-seq">
 
@@ -2860,6 +2871,7 @@ for more details and variations on this process.
 [`--np`]:                                             #bowtie2-options-np
 [`--offrate`]:                                        #bowtie2-options-o
 [`--omit-sec-seq`]:                                   #bowtie2-options-omit-sec-seq
+[`--sam-omit-prim-seq`]:                              #bowtie2-options-sam-omit-prim-seq
 [`--packed`]:                                         #bowtie2-build-options-p
 [`--phred33`]:                                        #bowtie2-options-phred33-quals
 [`--phred64`]:                                        #bowtie2-options-phred64-quals

NEWS

@@ -19,6 +19,12 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu
 Version Release History
 =======================
 
+## dev
+
+### bowtie2 ###
+  * Added option --sam-omit-prim-seq, which causes Bowtie 2 to set SEQ and QUAL
+    fields to "*" for primary alignments.
+
 ## Version 2.5.2 - Oct 13, 2023 ##
 
 ### bowtie2 ###

aln_sink.cpp

@@ -2054,7 +2054,8 @@ void AlnSinkSam::appendMate(
 		o.append("0\t");
 	}
 	// SEQ
-	if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
+	if(( flags.isPrimary() && samc_.omitPrimarySeqQual()  ) ||
+	   (!flags.isPrimary() && samc_.omitSecondarySeqQual())) {
 		o.append('*');
 	} else {
 		// Print the read
@@ -2070,7 +2071,8 @@ void AlnSinkSam::appendMate(
 	}
 	o.append('\t');
 	// QUAL
-	if(!flags.isPrimary() && samc_.omitSecondarySeqQual()) {
+	if(( flags.isPrimary() && samc_.omitPrimarySeqQual()  ) ||
+	   (!flags.isPrimary() && samc_.omitSecondarySeqQual())) {
 		o.append('*');
 	} else {
 		// Print the quals

bt2_search.cpp

@@ -131,6 +131,7 @@ static bool hadoopOut; // print Hadoop status and summary messages
 static bool fullRef;
 static bool samTruncQname; // whether to truncate QNAME to 255 chars
 static bool samAppendComment; // append FASTA/FASTQ comment to SAM record
+static bool samOmitPrimSeqQual; // omit SEQ/QUAL for primary alignments?
 static bool samOmitSecSeqQual; // omit SEQ/QUAL for 2ndary alignments?
 static bool samNoUnal; // don't print records for unaligned reads
 static bool samNoHead; // don't print any header lines in SAM output
@@ -344,6 +345,7 @@ static void resetOptions() {
 	fullRef		    = false;	// print entire reference name instead of just up to 1st space
 	samTruncQname       = true;	// whether to truncate QNAME to 255 chars
 	samAppendComment    = false;	// append FASTA/Q comment to SAM record
+	samOmitPrimSeqQual   = false;	// omit SEQ/QUAL for primary alignments?
 	samOmitSecSeqQual   = false;	// omit SEQ/QUAL for 2ndary alignments?
 	samNoUnal           = false;	// omit SAM records for unaligned reads
 	samNoHead	    = false;	// don't print any header lines in SAM output
@@ -541,6 +543,10 @@ static struct option long_options[] = {
 	{(char*)"sam-no-qname-trunc",          no_argument,        0,                   ARG_SAM_NO_QNAME_TRUNC},
 	{(char*)"sam-omit-sec-seq",            no_argument,        0,                   ARG_SAM_OMIT_SEC_SEQ},
 	{(char*)"omit-sec-seq",                no_argument,        0,                   ARG_SAM_OMIT_SEC_SEQ},
+	{(char*)"sam-omit-prim-seq",           no_argument,        0,                   ARG_SAM_OMIT_PRIM_SEQ},
+	{(char*)"omit-prim-seq",               no_argument,        0,                   ARG_SAM_OMIT_PRIM_SEQ},
+	{(char*)"sam-have-prim-seq",           no_argument,        0,                   ARG_SAM_HAVE_PRIM_SEQ},
+	{(char*)"have-prim-seq",               no_argument,        0,                   ARG_SAM_HAVE_PRIM_SEQ},
 	{(char*)"sam-no-head",                 no_argument,        0,                   ARG_SAM_NOHEAD},
 	{(char*)"sam-nohead",                  no_argument,        0,                   ARG_SAM_NOHEAD},
 	{(char*)"sam-noHD",                    no_argument,        0,                   ARG_SAM_NOHEAD},
@@ -871,6 +877,8 @@ static void printUsage(ostream& out) {
 	    << "  --rg <text>        add <text> (\"lab:value\") to @RG line of SAM header." << endl
 	    << "                     Note: @RG line only printed when --rg-id is set." << endl
 	    << "  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments." << endl
+	    << "  --sam-omit-prim-seq" << endl
+            << "                     put '*' in SEQ and QUAL fields for primary alignments." << endl
 	    << "  --sam-no-qname-trunc" << endl
 	    << "                     Suppress standard behavior of truncating readname at first whitespace " << endl
 	    << "                     at the expense of generating non-standard SAM." << endl
@@ -1292,6 +1300,8 @@ static void parseOption(int next_option, const char *arg) {
 	case ARG_SAM_NO_QNAME_TRUNC: samTruncQname = false; break;
 	case ARG_SAM_APPEND_COMMENT: samAppendComment = true; break;
 	case ARG_SAM_OMIT_SEC_SEQ: samOmitSecSeqQual = true; break;
+	case ARG_SAM_OMIT_PRIM_SEQ: samOmitPrimSeqQual = true; break;
+	case ARG_SAM_HAVE_PRIM_SEQ: samOmitPrimSeqQual = false; break;
 	case ARG_SAM_NO_UNAL: samNoUnal = true; break;
 	case ARG_SAM_NOHEAD: samNoHead = true; break;
 	case ARG_SAM_NOSQ: samNoSQ = true; break;
@@ -4940,6 +4950,7 @@ static void driver(
 			reflens,                // reference sequence lengths
 			samTruncQname,          // whether to truncate QNAME to 255 chars
 			samAppendComment,	// append FASTA/FASTQ comment to SAM record
+			samOmitPrimSeqQual,     // omit SEQ/QUAL for primary alignments?
 			samOmitSecSeqQual,      // omit SEQ/QUAL for 2ndary alignments?
 			samNoUnal,              // omit unaligned-read records?
 			string("bowtie2"),      // program id

doc/manual.html

@@ -2089,6 +2089,16 @@ <h4 id="sam-options">SAM options</h4>
 </td>
 </tr>
 <tr>
+<td id="bowtie2-options-sam-omit-prim-seq">
+<pre><code>--sam-omit-prim-seq</code></pre>
+</td>
+<td>
+<p>When printing primary alignments, Bowtie 2 by default will write
+out the <code>SEQ</code> and <code>QUAL</code> strings. Specifying this
+option causes Bowtie 2 to print an asterisk in those fields instead.</p>
+</td>
+</tr>
+<tr>
 <td id="bowtie2-options-omit-sec-seq">
 <pre><code>--omit-sec-seq</code></pre>
 </td>

doc/website/manual.ssi

@@ -2058,6 +2058,16 @@ about what fields are legal.</p>
 </td>
 </tr>
 <tr>
+<td id="bowtie2-options-sam-omit-prim-seq ">
+<pre><code>--sam-omit-prim-seq </code></pre>
+</td>
+<td>
+<p>When printing primary alignments, Bowtie 2 by default will write
+out the <code>SEQ</code> and <code>QUAL</code> strings. Specifying this
+option causes Bowtie 2 to print an asterisk in those fields instead.</p>
+</td>
+</tr>
+<tr>
 <td id="bowtie2-options-omit-sec-seq">
 <pre><code>--omit-sec-seq</code></pre>
 </td>

opts.h

@@ -162,6 +162,8 @@ enum {
 	ARG_ALIGN_PAIRED_READS,     // --align-paired-reads
 	ARG_SRA_ACC,                // --sra-acc
         ARG_SAM_APPEND_COMMENT,     // --sam-append-comment
+	ARG_SAM_OMIT_PRIM_SEQ,       // --sam-omit-prim-seq
+	ARG_SAM_HAVE_PRIM_SEQ,       // --sam-have-prim-seq
 };
 
 #endif

sam.h

@@ -63,6 +63,7 @@ class SamConfig {
 		const LenList& reflens,   // reference sequence lengths
 		bool truncQname,          // truncate read name to 255?
 		bool appendComment,	  // append FASTA/Q comment to sam record
+		bool omitprim,            // omit primary SEQ/QUAL
 		bool omitsec,             // omit secondary SEQ/QUAL
 		bool noUnal,              // omit unaligned reads
 		const std::string& pg_id, // id
@@ -108,6 +109,7 @@ class SamConfig {
 		bool print_zt) :
 		truncQname_(truncQname),
 		appendComment_(appendComment),
+		omitprim_(omitprim),
 		omitsec_(omitsec),
 		noUnal_(noUnal),
 		pg_id_(pg_id),
@@ -386,6 +388,17 @@ class SamConfig {
 	}
 
 
+        /**
+	 * Return true iff we should ignore the SAM spec's recommendations
+	 * and instead:
+	 *
+	 * SEQ and QUAL of primary alignments will be set to ‘*’ to reduce the
+	 * file size.
+	 */
+	bool omitPrimarySeqQual() const {
+		return omitprim_;
+	}
+
         /**
 	 * Return true iff we should try to obey the SAM spec's recommendations
 	 * that:
@@ -409,6 +422,7 @@ class SamConfig {
 
 	bool truncQname_;   // truncate QNAME to 255 chars?
 	bool appendComment_;// Append FASTA/Q comment to SAM record
+	bool omitprim_;     // omit primary
 	bool omitsec_;      // omit secondary
 	bool noUnal_;       // omit unaligned reads